ASAPbio preprint FAQ
Saturday sandbox · after Bourne (2005), "Ten simple rules for getting published"
In: LABLOOP-W15 Notebook
CARDS · WEEKS · THE WHOLE PLAN
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One box over every resource card and every document in the project. Type a thing you are stuck on.
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65 DOCUMENTS
Where the plan talks about it
- LABLOOP · Master Plan v6 — The Cartographer's Path: from program manager to published AI scientist for biotech
d memory. - **One cumulative notebook:** `LABLOOP-THESIS`. Only papers you cite, your own preprints, and `RELATED.md`. It replaces v5's "Bio / ML / Thesis" trio. ### Saturday build (last 20 minutes of the buffer block, for next week) 1. **Create** the notebook with the exact naroot89× - LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech
hings other scientists can check.** A repo with a DOI, a dataset other people download, a preprint with a method they can reproduce, a co-authored paper with a scientist who has a lab. Not talks, not posts, not certificates. Posts only amplify what the currency already bought. 3.root30× - Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4
[Instrument 1: batchlens\nfermentation batch intelligence] --> E[Evidence: repos, DOIs, 2 preprints, 4 deep dives, 3 videos] I2[Instrument 2: trialkit\ntrials and assays to decision] --> E I3[Instrument 3: labdocs\non-prem lab document intelligence] --> E V[Vara ideas: teleroot17× - Week 32 — paper 3 gate and career refresh
v5 Part 7 with retained v4 details. Deeper walkthrough: [v6 · Week 32 · GATE 32: Paper 3 preprint (L4 co-authored)](../../../LABLOOP-Master-Plan-v6.md#week-32--gate-32-paper-3-preprint-l4-co-authored). Active project/repository: enzymelens; portfolio; commercial materials. [Proexecution-plan/weeks/week-32-paper-3-gate-and-career-refresh15× - LABLOOP W16 — paper 1 preprint gate: full learning notebook
# LABLOOP W16 — paper 1 preprint gate: full learning notebook Prepared 2026-09-23 for Peter Ciancaglini. This is a study and execution guide; it does not record that you completed the work. Keep your existing noteexecution-plan/weeks/week-16-paper-1-preprint-gate14× - Week 16 — paper 1 preprint gate
# Week 16 — paper 1 preprint gate [**Full learning notebook: explanations, step-by-step challenges, stashes and evidence**](./learning-notebook.md) · [NotebookLM export](./notebooklm.txt) Status: NOT_STARTED.execution-plan/weeks/week-16-paper-1-preprint-gate14× - Programme progress
weeks/week-15-paper-1-review-and-revision/specs.md) — NOT_STARTED - [ ] Week 16: [paper 1 preprint gate](./weeks/week-16-paper-1-preprint-gate/specs.md) — NOT_STARTED - [ ] Week 17: [paper 2 complete experiments](./weeks/week-17-paper-2-complete-experiments/specs.md) — NOT_STARTEexecution-plan13× - Week 27 — loop audit offer and pipeline
ne-pager with scope, two-week effort assumptions, three candidates, one prototype and two preprints as proof. - Public/profile priority: Draft offer announcement grounded in evidence; update About to include audit clients and continue a distinct recruiter CTA. - Career/relationshexecution-plan/weeks/week-27-loop-audit-offer-and-pipeline7× - Week 19 — recruiter portfolio and review
this week sits.** - ← **From:** week 12 endorsement routes, week 15 reviewer, weeks 16-18 preprints and drafts. - → **Feeds:** week 20 (submission), week 27 (offer page links to the site), week 32 (second round of applications), week 37 (interviews). - ⟳ **Returns in:** every gatexecution-plan/weeks/week-19-recruiter-portfolio-and-review6× - Week 20 — paper 2 gate and halfway review
.md`. - 🏁 **This gate (20):** L4 endorsed. - 🌟 **Final:** the second half starts with two preprints, three instruments in motion and a network. **Mentor check.** *"I am an author of two preprints, one endorsed. I can present both without notes to a biologist and to an ML scientiexecution-plan/weeks/week-20-paper-2-gate-and-halfway-review6× - LABLOOP W32 — paper 3 gate and career refresh: full learning notebook
ek in plain language: what, why and where it leads Gate 32 requires a public co-authored preprint with real scientific contribution and author approval. Submission is an intermediate state. Alongside that work, you will refresh career evidence and shape the next engagement fromexecution-plan/weeks/week-32-paper-3-gate-and-career-refresh6× - LABLOOP W19 — recruiter portfolio and review: full learning notebook
ing programme.** - ← **From:** week 12 endorsement routes, week 15 reviewer, weeks 16-18 preprints and drafts. - → **Feeds:** week 20 (submission), week 27 (offer page links to the site), week 32 (second round of applications), week 37 (interviews). - ⟳ **Returns in:** every gatexecution-plan/weeks/week-19-recruiter-portfolio-and-review5× - LABLOOP W20 — paper 2 gate and halfway review: full learning notebook
dorsement, receipt and public ID independently. Stop when: Public ID satisfies the public-preprint gate; endorsement level requires actual endorsement. | | Tuesday | 90 min | Re-read all notes; Prompt P3 with "lab meeting" persona Produce: A 10-minute self-recorded explanation ofexecution-plan/weeks/week-20-paper-2-gate-and-halfway-review5× - LABLOOP — full weekly learning notebooks
iguration, result and known failure | | Scientific communication | W08 report | W16/20/32 preprints; W38 talk; W40 profile | A question, method, measured result and appropriately limited conclusion | The early concepts are tools you reuse. You do not need to relearn an entire unexecution-plan4× - Week 09 — fermlit scale up
- Scientific/build priority: Expand the screened corpus toward 2,000 papers; deduplicate preprint/journal versions and record exclusions and license restrictions. - Public/profile priority: Draft corpus-scale results with actual N and uncertainty around automated completeness esexecution-plan/weeks/week-09-fermlit-scale-up4× - LABLOOP W15 — paper 1 review and revision: full learning notebook
(../week-14-paper-1-full-draft/learning-notebook.md) · [Next notebook](../week-16-paper-1-preprint-gate/learning-notebook.md) ## 1. The week in plain language: what, why and where it leads Review is an attempt to find where the paper’s reasoning breaks. Model feedback can helpexecution-plan/weeks/week-15-paper-1-review-and-revision4× - LABLOOP W40 — final retrospective and career decision: full learning notebook
ecification.** This is Gate 40: **Evidence and decision**. Required proof: Three public preprints, one co-authored; two journal submissions; one JOSS submission; batchlens/trialkit/labdocs release DOIs; one delivered talk; at least one paid engagement delivered; written careerexecution-plan/weeks/week-40-final-retrospective-and-career-decision4× - Graph Report - biotech_skilling (2026-09-29)
Week 14 — paper 1 full draft - Week 15 — paper 1 review and revision - Week 16 — paper 1 preprint gate - Week 17 — paper 2 complete experiments - Week 18 — paper 2 full draft - Week 19 — recruiter portfolio and review - Week 20 — paper 2 gate and halfway review - Week 21 — protegraphify-out4× - Graph Report - biotech_skilling (2026-09-29)
Week 14 — paper 1 full draft - Week 15 — paper 1 review and revision - Week 16 — paper 1 preprint gate - Week 17 — paper 2 complete experiments - Week 18 — paper 2 full draft - Week 19 — recruiter portfolio and review - Week 20 — paper 2 gate and halfway review - Week 21 — protegraphify-out/2026-09-294× - Gates and evidence
at least one dated live endorsement conversation. | L2 | | 16 | Paper 1 | Public bioRxiv preprint DOI. Submission receipt alone leaves the public gate pending. | L3 when public | | 20 | Paper 2 | Public arXiv ID with endorsement, or scope-eligible bioRxiv public ID and a dated eexecution-plan3× - LABLOOP W09 — fermlit scale up: full learning notebook
---:|---| | Monday | 90 min | Expand the screened corpus toward 2,000 papers; deduplicate preprint/journal versions and record exclusions and license restrictions. Stop when: Every included paper has a stable identity and eligible full text. | | Tuesday | 90 min | NPTEL "Bioreactexecution-plan/weeks/week-09-fermlit-scale-up3× - Week 21 — protein study and partner scope
); ridge/GBM/MLP heads; baseline table | Partner call booked with the FermLit + batchlens preprints as the calling card - **Goal:** Paper 3 has a candidate partner, a dataset on disk and a baseline table. - **Tue (study):** FLIP thermostability task and Meltome atlas, deep read;execution-plan/weeks/week-21-protein-study-and-partner-scope3× - Week 37 — pilot or job process
w prep | Pilot (6-8 weeks) running, or interviews at scientific-data companies with three preprints | Weekly client readout - **Goal:** one concrete path is moving. - **Tue (study):** client domain reading or interview preparation (system design for scientific data, your papers aexecution-plan/weeks/week-37-pilot-or-job-process3× - Week 40 — final retrospective and career decision
* public retro posted. Plan Half 3 in one page, no more. - **Gate 40 passes when:** three preprints (one co-authored), two journal submissions, one JOSS submission, three instruments with DOIs, one talk delivered, at least one paid engagement delivered, and a decision written dowexecution-plan/weeks/week-40-final-retrospective-and-career-decision3× - Source reconciliation and feasibility decisions
on | Use the real report/dataset/draft link; update when public. | | Week 19 asks for two preprints before Paper 2's week 20 gate | Application assets label Paper 2 as manuscript/draft or submitted, as actually true. | | Week 16/20 goals alternate between submitted and public | Rexecution-plan2× - LABLOOP: week-by-week execution
and revision](./weeks/week-15-paper-1-review-and-revision/specs.md) | — | | 16 | [paper 1 preprint gate](./weeks/week-16-paper-1-preprint-gate/specs.md) | Paper 1 | | 17 | [paper 2 complete experiments](./weeks/week-17-paper-2-complete-experiments/specs.md) | — | | 18 | [paper 2execution-plan2× - LABLOOP v7 roadmap: hybrid, lead-first
e. ## Why the plan changed The v5/v6 plan was built to make a research scientist: three preprints, two journal submissions, a JOSS paper, three products, protein ML, extremophiles, field trials and a fund offer, all in 400 hours. Week 1 showed the real pace: a "30-minute" bioloexecution-plan2× - Week 16 commitment
nd date: not set. Available hours: confirm (planned ceiling 10). Primary outcome: paper 1 preprint gate. Minimum that keeps the next gate alive: the submission. ## Deliverables to commit - [ ] `paper-1-final-audit.md`: The author-approved manuscript has no unresolved essentialexecution-plan/weeks/week-16-paper-1-preprint-gate2× - Week 16 evidence register
ted | NOT_STARTED | Pending: Submission is documented; L3 is recorded only after a public preprint exists. | — | | paper-1-amplification.md | Not created | NOT_STARTED | Pending: Every draft uses the real public link or clearly says manuscript/submitted. | — | | Learning exerciseexecution-plan/weeks/week-16-paper-1-preprint-gate2× - Week 16 review and handoff
ps. Evidence: pending. - [ ] Submission is documented; L3 is recorded only after a public preprint exists. Evidence: pending. - [ ] Every draft uses the real public link or clearly says manuscript/submitted. Evidence: pending. - [ ] Learning assessed from Peter's actual answers.execution-plan/weeks/week-16-paper-1-preprint-gate2× - Week 17 — paper 2 complete experiments
-v6.md#week-17--paper-2-experiments-complete) · [Previous week review](../week-16-paper-1-preprint-gate/review.md) · [Next week](../week-18-paper-2-full-draft/specs.md) ## Outcome and relevance This week delivers the three concrete artifacts below and the supporting learning/brexecution-plan/weeks/week-17-paper-2-complete-experiments2× - Week 20 commitment
## Deliverables to commit - [ ] `gate-20-publication.md`: Public ID satisfies the public-preprint gate; endorsement level requires actual endorsement. - [ ] `talk-proposal.md`: A specific venue/date or search criteria and a ready proposal exist. - [ ] `halfway-retrospective.md`:execution-plan/weeks/week-20-paper-2-gate-and-halfway-review2× - Week 20 review and handoff
ce](./evidence.md) ## What was actually completed? - [ ] Public ID satisfies the public-preprint gate; endorsement level requires actual endorsement. Evidence: pending. - [ ] A specific venue/date or search criteria and a ready proposal exist. Evidence: pending. - [ ] Every gatexecution-plan/weeks/week-20-paper-2-gate-and-halfway-review2× - LABLOOP W27 — loop audit offer and pipeline: full learning notebook
ne-pager with scope, two-week effort assumptions, three candidates, one prototype and two preprints as proof. Stop when: Finish the fixed-scope Loop Audit one-pager and personalized follow-ups for the three strongest qualified leads. | | Tuesday | 90 min | Re-read v4 Part 4 and sexecution-plan/weeks/week-27-loop-audit-offer-and-pipeline2× - Week 32 review and handoff
What failed or changed, and why: pending. ## Gate and capacity Gate requirement: Public preprint DOI with a contributing scientist as co-author and all authors' approval. Gate status: NOT_STARTED. Original target week: 32. Actual completion date / forecast: not set. Missing extexecution-plan/weeks/week-32-paper-3-gate-and-career-refresh2× - LABLOOP W36 — journal and joss submissions: full learning notebook
ing: locate inputs and repair only the needed foundations - [Week 16](../week-16-paper-1-preprint-gate/specs.md): inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins. 1. Open the existing commitment and previous review/evideexecution-plan/weeks/week-36-journal-and-joss-submissions2× - Week 36 — journal and joss submissions
three in `PUBLICATIONS.csv`. - **Sun:** L-Sun "Three submissions: what changes between a preprint and a journal paper". - **Gate 36 passes when:** two journal submissions and one JOSS submission are logged. - **Only one thing:** the JOSS submission (fastest review, most useful fexecution-plan/weeks/week-36-journal-and-joss-submissions2× - Week 39 — fund portfolio offer
VIII · Threads: $, R · Next gate: 40** **Where this week sits.** - ← **From:** week 16 (preprint sent to GridX contact), week 27 (offer), weeks 29-30 and 32 (case study), v4 Part 4 (portfolio package pricing hypothesis). - → **Feeds:** week 40 (pipeline in the decision), Half 3execution-plan/weeks/week-39-fund-portfolio-offer2× - Week 40 review and handoff
ailed or changed, and why: pending. ## Gate and capacity Gate requirement: Three public preprints, one co-authored; two journal submissions; one JOSS submission; batchlens/trialkit/labdocs release DOIs; one delivered talk; at least one paid engagement delivered; written careerexecution-plan/weeks/week-40-final-retrospective-and-career-decision2× - Graph Report - biotech_skilling (2026-09-19)
Week 14 — paper 1 full draft - Week 15 — paper 1 review and revision - Week 16 — paper 1 preprint gate - Week 17 — paper 2 complete experiments - Week 18 — paper 2 full draft - Week 19 — recruiter portfolio and review - Week 20 — paper 2 gate and halfway review - Week 21 — protegraphify-out/2026-09-192×